METABOLISM OF ORGANIC AND

INORGANIC MATTERGunjan Mehta

Deptt. of Biotechnology,

Virani Science College, Rajkot

Metabolism of Organic matter 1. Fermentation 2. Respiration

1. Fermentation: “Special kind of redox reaction in which both electron donors and acceptors are organic in nature”. Internally generated organic compounds such as

pyruvic acid can serve as electron acceptor when external electron acceptor is absent.

Reduced compounds produced during such reactions are secreted in extracellular.

Fermentation yields less amount of ATP molecules than respiration, as in fermentation reaction organic compounds can’t be fully oxidized to CO2 & H2O.

Fermentation

In Fermentation, the organic compounds are simply rearranged into a form containing less energy than the organic substrate.

Fermentation generate few ATPs per molecule of substrate than respiration, hence more substrate molecules should be metabolize during it.

ATP synthesis during fermentation is substrate level phosphorylation and remains largely restricted to amount formed during glycolysis.

Chemiosmotic synthesis and oxidative phosphorylation of ATP don’t occur in fermentation.

Fermentation

Respiration

“Biochemical process in which organic compound serve as electron donor while external compound serve as terminal electron acceptor”. R

esp

irati

on Aerobic

Anaerobic

Aerobic Respiration When O2 serve as terminal electron

acceptor.

Anaerobic respiration

Instead of O2 other inorganic compound serve as terminal electron acceptor.

Anaerobic Metabolism

Terminal Electron acceptor

Product Example

Anaerobic respiration

Fe3+, S Fe2+,

H2SDenitrifiers,

Sulfur reducers etc

Denitrification

NO3-, NO2

- NO2, N2O, N2

Paracoccus denitrifucans

Sulfate reduction

SO42- H2S Desulfovibrio

desulfuricans

Methanogenesis

CO2 CH4 Methanococccus spp

Aerobic Vs Anaerobic respiration Aerobic respiration is very imp process in

bioremediation as various organic compounds will be fully oxidized and converted to inorganic minerals. In bacteria this procedure involves enzymes capable of adding O2.

1. Monooxygenase- one O2 molecule 2. Dioxygenase- two O2 molecule Anaerobic respiration: Carried out by

obligatory anaerobes and facultative anaerobes. O2 will be given preference.

Fermentation vs Respiration

Respiration is more efficient than fermentation because of following reasons…

1. The difference in reducing potential between the primary electron donor and terminal electron acceptor is high.

2. In respiration complete oxidation of organic matter will occur compared to fermentation where incomplete oxidation will occur.

Metabolism of Inorganic matter

1. Nitrate reduction 2. Sulfate reduction 3. Lithotrophy: a) Hydrogen bacteria b)

Sulfur bacteria

Mainly followed during anaerobic respiration by Nitrate reducing bacteria, Sulfate reducing bacteria and many other lithotrophic bacteria.

These metabolic pathways are the most integral parts of Biogeochemical cycles.

Nitrate reduction/ Denitrification Nitrate reduction takes place through both assimilatory

and dissimilatory cellular functions. Assimilatory denitrification: nitrate is reduced to

ammonia, which then serves as a nitrogen source for cell synthesis. Thus, nitrogen is removed from the liquid stream by incorporating it into cytoplasmic material.

Dissimilatory denitrification: nitrate serves as the electron acceptor in energy metabolism and is converted to various gaseous end products but principally molecular nitrogen, N2, which is then stripped from the liquid stream.

A relatively small fraction of the nitrogen is removed through assimilation. Dissimilatory denitrification is, therfore, the primary means by which nitrogen removal is achieved.

Nitrate reduction

A carbon source is also essential as electron donor for denitrification to take place..

Denitrification releases nitrogen which escapes as an inert gas to the atmosphere while oxygen released stays dissolved in the liquid and thus reduces the oxygen input needed into the system. Each molecule of nitrogen needs 4 molecules of oxygen during nitrification but releases back 2.5 molecules in denitrification. Thus, theoretically, 62.5% of the oxygen used is released back in denitrification.

Assimilatory denitrification

Nitrate is reduced to ammonia, which then serves as a nitrogen source for cell synthesis. Thus, nitrogen is removed from the liquid stream by incorporating it into cytoplasmic material.

Assimilatory denitrification

Assimilatory denitrification

Since oxidation state of nitrogen in nitrate is +5 and in ammonia it is -3. Total 8 e- must be transferred to nitrate in order to reduce it to ammonia.

Dissimilatory denitrification In dissimilatory denitrification, nitrate serves

as the electron acceptor in energy metabolism and is converted to various gaseous end products but principally molecular nitrogen, N2, which is then stripped from the liquid stream.

Dissimilatory denitrification is the primary means by which nitrogen removal is achieved.

Dissimilatory denitrification

Dissimilatory denitrification Nitrogenous oxides, principally NO3-, NO2- are

used as terminal electron acceptor in the absence of O2 and reduced molecular nitrogen N2 during microbial metabolism.

Enzymes for denitrification procedure are oxygen sensitive and works under anaerobic condition.

All denitrifying organisms are facultative anaerobes such as Pseudomonas and Alcaligens.

Achromobacter, Vibrio, Flavobacterium

Sulfate reduction

SO42-( most oxidized form of S) can be used as terminal

electron acceptor by a specialized group of microbes which are known as Sulfur reducing bacteria….

SO42- first reduced to sulfite(SO3

- ) and then to sulfide(H2S) or S2- and then incorporated into Cysteine.

The oxidation level of S in SO42- is (+6) and in sulfide it

is (-2), so total 8 electrons are required to reduce SO42-

to S2-. Gram +ve: Desulfotomaculum Gram –ve: Desulfovibrio Archaebacteria: Archaeglobus

Assimilatory sulfate reduction

Adenosine-PO2-PO2-PO3+ SO42-

-PPi ATP sulfurylase Adenosine- PO3 –SO3

Adenosine phosphosulfate (APS)/ AMP-SO2

APS phosphorylase Phosphoadenosine phosphosulfate/ SO3- -

AMP- SO2

-AMP-3’-P PAPS reductase SO3

-2

Assimilatory sulfate reduction

SO3-2

3NADPH3NADP Sulfite reductase H2S +O- acetyl serine

-acetate acetyl serine sulfhydrilase L- Cysteine

Assimilatory sulfate reduction

Assimilatory sulfate reduction

There is sound thermodynamic reason behind the formation of APS, which is AMP derivative of sulfate.

The reduction potential of sulfate can be increased by attaching AMP, which makes it a better electron acceptor than free sulfate.

Formation of PAPS: The reductant is sulfhydryl protein called thioridoxin, which accepts e- from NADPH.

3 ATP molecules are used: a. 2 ATP for PAPS b. 1 ATP for AMP formation

Dissimilatory sulfate reduction

Dissimilation of sulfate is very rare as it yields less amount of energy than any alternative e- donor as nitrate or oxygen.

Since energy influences growth and metabolism of these SRBs, it shows slow growth.

Comparative pathways

Lithotrophy

The study of metabolism of organism using reduced inorganic material is called lithotrophy.

CO2- Lithoautotrophs(Most of) H2, NH3, H2S, NO2, Fe+2, CO-

Lithotrophs(Some) Consist of one of the major class of

autolithotrophs and very important for it.

Classification of lithotrophs

1. Hydrogen bacteria:

Sulfur oxidizing bacteria:

e- donor

e-accept

or

Final Product

Example

H2 O2 H2O Alkaligens eutrophus

e- donor

e-accepto

r

Final Product

Example

H2S, S2-, S2O3

O2 SO42- Thiobacillus

thioxidans, Baggiatoa

Classification of lithotrophs

3. Iron oxidizing bacteria

4. Nitrogen oxidizing bacteriaa. Ammonia oxidizing:

e- donor

e-accepto

r

Final Product

Example

Fe+3 O2 SO42- Thiobacillus

thioxidans,

e- donor

e-accepto

r

Final Product

Example

NH4+ O2 N2O, NO-, NO2, NO3-

Nitrosomonas eutropy

Classification of lithotrophs

3. Iron oxidizing bacteria

4. Nitrogen oxidizing bacteriaa. Ammonia oxidizing:

e- donor

e-accepto

r

Final Product

Example

Fe+3 O2 SO42- Thiobacillus

thioxidans,

e- donor

e-accepto

r

Final Product

Example

NH4+ O2 N2O, NO-, NO2, NO3-

Nitrosomonas eutropy

Classification of lithotrophs

b. Nitrite oxidizing:

5. Methanogens

e- donor

e-accepto

r

Final Product

Example

NO2- O2 NO3- Nitrobacter

winograsky e-

donore-

acceptor

Final Product

Example

H2 CO2, Acetate

, Methyl

CH4 Methanococcus spp

Classification of lithotrophs

6. Methylotrophse-

donore-

acceptor

Final Product

Example

CH4 CO2 Organic compoun

d

Methylococcus

Hydrogen bacteria

Facultative lithotrophs Also known as hydrogen oxidizing bacteria

capable of utilizing H2 as source of energy. Majority of these bacteria are aerobic

capable of utilizing O2 as terminal e- acceptor.

However they are not purely dependent on H2 as energy source but are capable of utilizing other organic sources. That’s why it is facultative lithotrophs.

CO2+ 2H2[CH2O]n+H2O Hydrogen is oxidized by membrane bound

hydrogenase.

Sulfur oxidizing bacteria

It includes….1. Photosynthetic sulfur oxidizers: Green sulfur

bacteria & purple sulfur bacteria2. Non- Photosynthetic sulfur oxidizers: colourless

sulfur bacteria such as Baggiatoa, Thiothrix Almost all are gram –ve e- donors for SOBs: H2S, S2-, S2O3

Comprises physiologically diverse group of bacteria:1. Obligatory autotrophs(CO2- sole C source)

2. Facultative heterotrophs(Mixotrophic) Eg: Baggiatoa

Sulfur oxidizing bacteria

On the basis of pH requirement:1. Neutrophile: pH= 7.02. Acidophile: pH= 1- 5 (Thiobacillus thioxidans)

S2-/ H2S

[S]- linear polysulfate Sulfur oxidase/ sulfite oxidase

SO32- APS

APS

SO42-

Sulfur oxidizing bacteria

Few sulfur oxidizing bacteria are archaebacteria such as Sulfolobus.

Lives on sulfur rich spring- hot spring in temperature range upto 90º C and pH=1.

H2S+2CO2 SO42- + 2H+

S+ H2O+O2 SO42-+ 2H+

S2O3+ H2O+2O2 SO42- + 2H+